The aim of this study was to characterize the gene expression profiles of mouse testis at different stages by performing large-scale complementary DNA (cDNA) analysis using DNA microarrays. The transcription profile of mouse testis was determined by comparing testis samples of mice aged 4, 9, 18, 35, 54 d and 6 months using Affymetrix Genechip mouse microarrays (430 v.2). Of the six comparative pairs of two neighboring spots examined, lots of differently expressed genes existed on day 18 versus day 9 and on day 35 versus day 18, indicating these genes may be involved in unique events during those periods. In mining the Genechip data, the gene expression profiles of 2058 genes represented in a gradually increased manner in the developmental stages of mice testis, and its validity was confirmed by the data of 21 known spermatogenesis-related testis-specific genes in our chip and the results of 10 random sample from 2058 genes produced by the sub-quantitative RT-PCR. So, we called these 2058 genes spermatogenesis-related genes. By informatics analysis, the gene expression clustering, gene ontology, KEGG pathway and domain regions were predicted for describing the potential roles that may play during mouse spermatogenesis. This study provides a molecular basis for the identity of spermatogenesis-related gene in mouse testis and leads to the elucidation of the molecular events underlying mammalian male reproduction.